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United States Department of Agriculture

Agricultural Research Service

Research Project: Efficient Management and Use of Animal Manure to Protect Human Health and Environmental Quality

Location: Food Animal Environmental Systems Research Unit

2013 Annual Report

1a.Objectives (from AD-416):
The overall goal of the research project which is formulated as a real partnership between ARS and Western Kentucky University (WKU) is to conduct cost effective and problem solving research associated with animal waste management. The research will evaluate management practices and treatment strategies that protect water quality, reduce atmospheric emissions, and control pathogens at the animal production facilities, manure storage areas, and field application sites, particularly for the karst topography. This Project Plan is a unique situation in the sense that non-ARS scientists from WKU are included on an in-house project to conduct research under the NP 214. The objectives and related specific sub-objectives for the next 5 years are organized according to the Components (Nutrient, Emission, Pathogen, and Byproduct) of the NP 214, which mostly apply to this project as follows:.
1) develop improved best management practices, application technologies, and decision support systems for poultry and livestock manure used in crop production;.
2)develop methods to identify and quantify emissions, from poultry, dairy and swine rearing operations and manure applied lands;.
3)reduce ammonia, odors, microorganisms and particulate emissions from dairy, swine and poultry operations through the use of treatment systems (e.g. biofilters and scrubbers) and innovative management practices;.
4)perform runoff and leaching experiments on a variety of soils amended with dairy, swine, or poultry manures infected with Campylobacter jejuni (C. jejuni), Salmonella sp. or Mycobacterium avium subsp. paratuberculosis (MAP) and compare observed transport with that observed for common indicator organisms such as E. coli, enterococci, and Bacteriodes; and.
5)use molecular-based methodologies to quantify the occurrence of pathogens and evaluate new methods to inhibit their survival and transport in soil, water, and waste treatment systems.

1b.Approach (from AD-416):
This in-house project was conceived as a cooperative/partnership and comprehensive research program between USDA-ARS Animal Waste Management Research Unit (AWMRU) and Western Kentucky University (WKU). The project is designed to utilize the scientific expertise and facilities of both institutions to conduct problem-solving research related to animal waste management in Kentucky and the southeastern U.S. The research effort will be multi-disciplinary and multifaceted in support of decision making and systems development. Research focuses will be on all four components (Nutrient, Atmospheric Emission, Pathogens, and By-products) of the National Program 214. In lieu of repeatedly stating the equipment used for analysis, please note that the state-of-the-art laboratories and equipments exist at both AWMRU and WKU, which can be accessed by the scientists including land at the WKU research station. Main instruments include: ICP, GC-MS, 2 GCs, Latchet, 2 C/N Analyzers, IC, HPLC, Real-time PCR, etc.

3.Progress Report:
This project plan under several objectives/sub-objectives investigates environmental problems related to the improper use of animal manure and agricultural waste in relation to nutrients, pathogens, greenhouse gases (GHGs), odor-causing compounds, dust and sediment associated with animal production facilities and manure application sites. Research also determines best management practices (BMPs) for crop production on land receiving agricultural waste with regard to crop management and soil types particularly in this unique “karst topography” region. Following are research related activities for the past year: Completed the 2nd year of a study to evaluate the survival of naturally occurring pathogens (Campylobacter jejuni, Listeria monocytogenes and Salmonella enterica) and indicator organisms (Escherichia coli [E. coli], enterococci) in applied poultry litter or dairy manure. A new collaboration was established with the University of Kentucky evaluating the transport of E. coli strains with different adhesion properties through karst systems. The National Pork Board Research has provided funding to investigate the effects of manure application rate and timing on transport of antibiotic resistant bacteria through soils. Gas quality and dissolved gases in anaerobic digesters are being studied. Concentrations of methane and carbon dioxide in the biogas produced by anaerobic digestion of swine waste and other agricultural wastes are quantified in conjunction with those of dissolved methane, carbon dioxide and bicarbonate in wastewater. Initiated a study to quantify antibiotics in swine manure. Four antibiotics (penicillin, tetracycline, chlortetracycline and oxytetracycline) that are commonly added to swine feed to prevent disease and promote weight gain are being studied to determine their concentrations at all stages of swine production from birth to slaughter. Also, ARS scientists at Bowling Green, KY, initiated collaboration with ARS scientists in Lincoln, NE, to optimize methods and procedures for extracting and amplifying antibiotic resistant (AR) bacteria and their genes in agricultural matrices. An ARS scientist at Bowling Green, KY, has developed assays to target 5 different groups of AR genes (tetracyclines, sulfonamides, erythromycin, ampicillin and streptomycins). ARS scientists in Bowling Green deployed the ambient ion monitor method (AIM) to detect gas and particle phase amines and gas phase sulfur compounds at a swine facility in Kentucky. Also, Smog chamber experiments on amines were conducted in collaboration with the University of California at Riverside. The swine manure composting study is still underway; also measuring the ammonia and greenhouse gases from swine manure compost systems to see the effect of management on the potential emissions. Research is being conducted in collaboration with researchers at eight major universities to compare and evaluate accuracy of phosphorus indices from 10 states using water quality monitoring data collected in multiple watersheds using and predictions of P loss from these watersheds using fate-and-transport models.

1. Use of biochar to increase Escherichia coli (E. coli) retention in soils. The land application of animal and human fecal material poses a potential public health risk if humans become exposed to fecal-borne pathogenic microorganisms such as bacteria, viruses, and protozoa. One potential route of transmission for these pathogenic microorganisms is through drinking fecally-contaminated groundwater. One management practice which has the potential for reducing contamination of groundwater supplies by pathogenic microorganisms is amending soils with charred organic matter derived from plant biomass or bio-waste. This material, termed biochar, has been proposed as a means to sequester carbon from the atmosphere. ARS scientists from Bowling Green, KY, in collaboration with the University of California at Riverside conducted experiments to compare the effect of different types of biochar on the surface properties and transport behavior Escherichia coli (E. coli) through soil columns. Results showed that the source of biochar can have a strong impact on the mobility of E. coli through soil. Specifically, biochar produced from pine chips was found to be much more effective in restricting E. coli transport than biochar produced from poultry litter.

2. Pathogens responsible for Johne’s disease and gastroenteritis are surprisingly resistant to ensiling process. Livestock production relies heavily on silage materials as feed during winter months. The low potential of hydrogen (pH) and high organic acid concentrations produced during ensiling result in a well-preserved highly nutritious feedstock. However, organisms that exhibit acid tolerance may survive the ensiling process and can be a concern for food and animal safety when contaminated materials are fed to livestock. Researchers at the ARS in Bowling Green, KY, and from the Miner Agricultural Research Institute in Chazy, NY, evaluated the susceptibility of two acid tolerant pathogens to silage conditions. Mycobacterium avium subsp paratuberculosis (M. paratuberculosis) causes Johne’s disease in cattle and Salmonella enterica serotype Typhimurium (S. Typhimurium) is a common human gastrointestinal pathogen. Researchers found that while S. Typhimurium was relatively sensitive to ensiling M. paratuberculosis was especially resistant, surviving longer and in higher concentrations. These results suggest that when present in manure and applied to forage grasses that are ensiled, M. paratuberculosis may survive the ensilaging process and could, therefore, be a potential route of infection if ingested by a susceptible animal.

3. Antibiotic resistance (AR) genes, pathogens and indicator organisms in land applied manures. ARS researchers in Bowling Green, KY, working in collaboration with scientists at Western Kentucky University applied poultry litter and dairy manure to forage grasses under conventional and no till management. They found that even when gastrointestinal pathogens like Campylobacter jejuni and Salmonella enterica were present in manures at high concentrations initially, they were rarely detectable following land application. Indicator organisms like enterococci were measurable but the common indicator Escherichia coli (E. coli) was not. They found that Antibiotic resistance (AR) genes were very high in poultry litter before application and concentrations remained high following land application of litter. Detection of AR genes, pathogens and indicators following manure application was irregular over the sampling period suggesting that factors such as moisture and temperature play an important role in persistence in soil. This information should be considered in any risk assessment model and is important for stakeholders using livestock manures for land application onto forage grasses.

4. Improvements in wastewater biogas production. Methane is produced by the breakdown of animal manures in the absence of oxygen. This methane remains a largely untapped source of energy due to the corrosive nature of the gas. Hydrogen sulfide and carbon dioxide are the major contaminants of the natural gas produced by the microbial breakdown of animal wastes. These compounds reduce the heating value of the gas and lead to costly maintenance problems. ARS researchers in Bowling Green, KY, circulated wastewater from an anaerobic digester through a silicone hose located in an external tank. The tank was filled with a buffer solution designed to remove carbon dioxide from the wastewater. This treatment reduced carbon dioxide concentrations in the biogas resulting in a fuel with higher heating value. Improved processes for the production of biogas can lead to significant energy savings for producers and industry as well as reduced greenhouse gas emissions to the environment.

5. Development of a new phosphorus (P) index for Kentucky. In most states, the phosphorus (P) index is the adopted strategy for assessing a field’s vulnerability to P loss as required by the USDA-NRCS 590 Nutrient Management Standard. Recently, USDA-NRCS revised its 590 Standard to require that states demonstrate the accuracy of their P index. Previous research by ARS researchers in Bowling Green, KY, identified several important limitations with the existing P index for Kentucky (KY). As a result, ARS was asked to lead an effort to develop a new P index for KY with representatives from the University of KY, KY USDA-NRCS, KY Division of Water, and KY Division of Conservation. A new P index was developed to reflect current understandings of the processes controlling P loss at the field scale. The new P index was evaluated against P runoff data reported in the literature and was shown to provide significantly better predictions of P loss from agricultural fields than the original KY P index. The new index provides users with a more accurate tool for assessing the risk of P loss from agricultural fields. The new P index has been adopted by Kentucky USDA-NRCS as part of their 590 Nutrient Management Standard.

6. Developing methods for evaluating the accuracy of a phosphorus (P) index. A phosphorus index (PI) is a very simple tool used by most states to evaluate the risk of phosphorus (P) leaving agricultural fields and entering streams and lakes where it may cause water-quality deterioration. While the PI is a commonly used tool, most state P indices have not been rigorously evaluated against measured P loss data to determine how well the PI assigns P loss risk – a major reason being the lack of field data available for such an analysis. Given the lack of P loss data available for PI evaluation, ARS scientists from Bowling Green, KY, and other units demonstrated a method for evaluating P indices using output from more complex P loss models. Applying this approach to an existing state P index, ARS researchers from Bowling Green, KY, were able to identify several potential limitations with a commonly used formulation of the P index. Moreover, results from this research showed how this new approach can be used to improve how each factor in the P index is weighted. Results from this research have been used to inform developers modifying P indices in Kentucky, Maryland, Oregon, and Washington.

7. Incorporating uncertainties in predictions from phosphorus loss models. Models are often used to predict phosphorus (P) loss from agricultural fields. While it is commonly recognized that model predictions are inherently uncertain, few studies have addressed prediction uncertainties using P loss models. Research conducted by ARS scientists in Bowling Green, KY, evaluated two methods for assessing uncertainties in the Annual P Loss Estimator (APLE) model, a commonly used model developed by ARS for evaluating P loss from agricultural fields. This research resulted in identifying a simple method for calculating prediction uncertainties for the APLE model. The research also demonstrated the range in magnitude of model prediction uncertainties associated with uncertainties in model input variables. In particular, results showed that prediction uncertainties due to errors in model inputs can range from ± 2 to 64% of the predicted value. Because the APLE model has been used to evaluate the accuracy of P loss models and to identify practices which help minimize P loss from agricultural fields, implementation of uncertainty to model predictions will provide improved estimates of P loss when using this model.

8. Corn Response to Enhanced-Efficiency Nitrogen Fertilizers (EENF) and Poultry Litter. Nitrogen (N) is one of the most important nutrients and costly input for crop production. Farmers are looking for better management practice to enhance N utilization and crop production while reducing environmental impact. ARS scientists in Bowling Green, KY, have investigated corn (Zea mays L.) grain yield and nutrient uptake resulting from application of 168 kg N ha-1 of several inorganic N fertilizers, commercially available Enhanced-Efficiency Nitrogen Fertilizers (EENF), and poultry litter under no-till corn production. All N sources increased corn grain yield over control (no N applied), however, no significant differences were observed among the EENF and other N fertilizer sources. This research will help farmers with needed scientific information, because lack of research-based recommendations as to when and where these EENF would be most effective, and which combination of management practices would optimize their performances.

9. Association of odors (volatile fatty acids) in suspended particulate matters from poultry house air emissions. As more and more animal production continues to evolve into major concentrated operations, odor emissions from these confined animal feeding operations (CAFOs) have caused persistent public concern and complaints. In addition, particulate matters and other gas emissions have also been a cause for environmental and health concerns. Researchers from ARS in Bowling Green, KY, conducted experiments to understand the association of odors in suspended particulate matters from poultry houses to examine and characterize the profile of various volatile fatty acids in the inhalable fractions of suspended particulate matters from a poultry house that used rice hulls as bedding materials over a period of one flock. The results showed that propionic and butyric acid are the major volatile fatty acids found in the inhalable fraction of dust collected from the broiler house after a total cleanout. Trace amounts of other volatile fatty acids (i.e., acetic acid, pentanoic acid, and hexanoic acid) were also observed from particulate matter analyses. Based on these data, particulate matters could serve as potential carriers for short and long-range transport of odorous compounds such as volatile fatty acids.

Review Publications
Bolster, C.H., Vadas, P.A., Sharpley, A.N., Lory, J.A. 2012. Using a P loss model to evaluate and improve P indexes. Journal of Environmental Quality. 41:1758-1766.

Sharpley, A., Beegle, D., Bolster, C.H., Good, L., Joern, B., Ketterings, Q., Lory, J., Mikkelsen, R., Osmond, D., Vadas, P.A. 2012. Phosphorus indices: Why we need to take stock of how we are doing. Journal of Environmental Quality. 41(6):1711-1719.

Osmond, D., Cabrera, M., Sharpley, A., Bolster, C.H., Feagley, S., Lee, B., Mitchell, C., Mylavarapu, R., Oldham, L., Walker, F., Zhang, H. 2012. Comparing southern P indices to runoff data. Journal of Environmental Quality. 41:1741-1749.

Cook, K.L., Flis, S.A., Ballard, C.S. 2013. Mycobacterium avium subsp paratuberculosis cells are surprisingly resistant to ensiling process. Paratuberculosis Newsletter. March 2013 p7-8.

Erupe, M.E., Liberman-Martin, A., Silva, P.J., Malloy, Q.G., Yonis, Y., Cocker, III, D.R., Purvis-Roberts, K. 2010. Determination of Methylamines and Trimethylamine-N-oxide in particulate matter by non-suppressed ion chromatography. Journal of Chromatography. 1217(13):2070-2073.

Loughrin, J.H., Bolster, C.H., Lovanh, N.C., Sistani, K.R. 2010. A simple device for the collection of water and dissolved gases at defined depths. Applied Engineering in Agriculture. 26(4):559-564.

Quintanar, A.I., Mahmood, R., Loughrin, J.H., Lovanh, N.C., Motley, M.V. 2009. A system for estimating bowen ratio And evaporation from waste lagoons. Applied Engineering in Agriculture. 25(6):923-932.

Loughrin, J.H., Quintanar, A., Mahmood, R., Lovanh, N.C. 2010. Heat flux measurements and modeling of malodorous compounds above an anaerobic swine lagoon. Water, Air, and Soil Pollution. 217(1-4):463-471.

Sistani, K.R., Mikha, M.M., Warren, J.G., Gilfillen, B., Acosta Martinez, V. 2011. Nutrient source and tillage impact on corn grain yield and soil properties. Soil Science. 175(12):593-600.

Gilfillen, R.A., Rowland, N.S., Willian, W.T., Sleugh, B.B., Tekeste, M.Z., Sistani, K.R. 2010. Effects of broiler litter application on nutrient accumulations in soil.. Forage and Grazinglands. doi:10.1094/FG-2010-1105-01-RS.

Jn-Baptiste, M., Sistani, K.R., Tewolde, H. 2012. Poultry manure application time impact on corn grain production in a crider silt loam. Soil Science. 177(1):47-55.

Cook, K.L., Bolster, C.H., Ayers, K.A., Reynolds, D.N. 2011. Escherichia coli diversity in livestock manures and agriculturally impacted stream waters. Current Microbiology. 63(5):439–449.

Gilfillen, B., Rowland, N., Willian, T., Sleugh, B.B., Tekeste, M.Z., Sistani, K.R. 2010. Effects of broiler litter application on nutrient accumulation in soil. Forage and Grazinglands. On Line Only- doi:10.1094/FG-2010-1105-01-RS.

Bolster, C.H. 2011. A critical evaluation of the Kentucky phosphorus index. Journal of the Kentucky Academy of Science. 72(1):46–58.

Loughrin, J.H., Quintanar, A.I., Cook, K.L., Lovanh, N.C., Mahmood, R., Bexerra-Acosta, E. 2012. Seasonal variation in heat fluxes, predicted emissions of malodorants, and wastewater quality of an anaerobic swine waste lagoon. Water, Air, and Soil Pollution. 223:3611–3618.

Last Modified: 4/15/2014
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